Bruise pain sensation in my right foot - an adjustment fix?

After fitting clipless pedals to my bike Iím experiencing a problem in my right foot.
For example if I go for a ride I end up with a discomfort/light pain in the ball of the foot behind the second and third smallest toes. The best way I can describe it is like a bruising where the sensation will increase over a day or so and then subside in the following days as if it cures.
Iím perfectly happy with how my foot sits over the axle of the pedal so that leaves me with three more adjustment options; toe-in/out, left & right and shoe strap tightness.
What I canít tell is whether it is due to the pressure from the contact point or if it is a lack of this and they donít have support.
I donít have any problems with my left foot at all.
Any ideas?